Installing glTF-Blender-IO latest Version in Blender 2.8
I'll start off by saying, Blender 2.80 Beta and the GitHub glTF-Blender-IO repository are going to be kept in sync at least through the end of 2.80's release and likely far beyond.  So if something new goes in the GitHub master branch, usually you can wait a couple of days and see it show up in a daily build of Blender.  There's a version number near the top of __init__.py that has been getting more regular updates, with the intention of making it more apparent when GitHub changes have made their way into the Blender repo.

What I'm saying is, if there's no rush on your part, you can just wait for the changes to come through on the Blender side, and not worry about downloading from GitHub.

But, if you want to try something before it gets over to Blender (such as a branch that's under development, or a fix you need right away, etc.), then yes, download the GitHub repository and install the addons/io_scene_gltf2 folder from there.

The trickiest thing about the install will be that Blender can't tell the difference between the shipped addon vs the one you downloaded.  You need to get rid of the copy that came pre-installed with Blender, before you can try a new branch or version of the same addon.  In your Blender install folder, look for this subfolder:

{Blender_Install_Folder}/2.80/scripts/addons/io_scene_gltf2/


This one needs to be deleted or moved completely out of the Blender install tree, before you can replace it with a new one.  The addons/io_scene_gltf2 folder from GitHub can be used as a drop-in replacement here, if you like, or you can use one of the external script folder methods you mentioned above.

Quit and re-start Blender to make these changes apply.  Note that you will not have to go re-enable the addon, even if it's in a different install folder.  Apparently, Blender keeps a list of enabled addons by name, not by install location, so your new version of this addon will already be enabled when you launch Blender.